-
westram
2008-06-18 11:42
#24
Rev.: 5407
-
7 lines of code changed in 1 file:
-
ARBDB:
adlang1.c (+7 -11)
-
westram
2008-06-18 11:42
#23
Rev.: 5406
-
6 lines of code changed in 1 file:
-
westram
2008-06-18 11:42
#22
Rev.: 5405
-
51 lines of code changed in 10 files:
-
ALIV3:
a3_seq.cxx (+8 -14)
-
AWT:
AWT_tree.cxx (+12 -18),
awt_tree.hxx (+1 -1)
-
AWTC:
AWTC_constructSequence.cxx (+13 -22)
-
DIST:
DI_matr.cxx (+1 -1)
-
MULTI_PROBE:
MP_noclass.cxx (+3 -10)
-
NALIGNER:
ali_aligner.cxx (+7 -10),
ali_prealigner.cxx (+2 -5)
-
PARSIMONY:
AP_tree_edge.cxx (+2 -5)
-
PROBE_SERVER/WORKER:
psw_main.cxx (+2 -4)
-
westram
2008-06-18 10:49
#21
Rev.: 5404
-
1 lines of code changed in 1 file:
-
EDIT4:
ED4_main.cxx (+1 -1)
-
westram
2008-06-18 10:48
#20
Rev.: 5403
-
709 lines of code changed in 2 files:
-
EDIT4:
ED4_protein_2nd_structure.cxx (+701 -332),
ed4_protein_2nd_structure.hxx (+8 -387)
-
westram
2008-06-18 09:02
#19
Rev.: 5402
-
1 lines of code changed in 1 file:
-
DIST:
DI_save_matr.cxx (+1 -1)
-
westram
2008-06-18 09:01
#18
Rev.: 5401
-
1 lines of code changed in 1 file:
-
westram
2008-06-18 09:01
#17
Rev.: 5400
-
3 lines of code changed in 2 files:
-
NTREE:
NT_validNameParser.cxx (+2 -2)
-
PROBE_SET:
ps_convert_db.cxx (+1 -1)
-
westram
2008-06-18 09:01
#16
Rev.: 5399
-
29 lines of code changed in 8 files:
-
PROBE_SET:
fb_test.cxx (+4 -4),
ps_arb2asciipaths.cxx (+1 -1),
ps_candidate.hxx (+5 -5),
ps_detect_weak_differences.cxx (+8 -8),
ps_eval_candidates.cxx (+3 -3),
ps_find_probes.cxx (+6 -6),
ps_my2asciipaths.cxx (+1 -1),
ps_node.hxx (+1 -1)
-
westram
2008-06-17 15:48
#15
Rev.: 5398
-
27 lines of code changed in 1 file:
-
westram
2008-06-17 15:48
#14
Rev.: 5397
-
7 lines of code changed in 1 file:
-
lib/addlibs:
install_libs.sh (+7 -3)
-
westram
2008-06-10 19:15
#13
Rev.: 5396
-
4 lines of code changed in 2 files:
-
MERGE:
MG_main.cxx (+2 -2)
-
WINDOW:
AW_xkey.cxx (+2 -2)
-
westram
2008-06-10 19:14
#12
Rev.: 5395
-
4 lines of code changed in 1 file:
-
westram
2008-06-10 19:14
#11
Rev.: 5394
-
27 lines of code changed in 2 files:
-
ARBDB:
adlocal.h (+21 -19),
arbdb.h (+6 -4)
-
westram
2008-06-10 19:14
#10
Rev.: 5393
-
19 lines of code changed in 1 file:
-
ARBDB:
adhash.c (+19 -26)
-
westram
2008-06-10 16:29
#9
Rev.: 5392
-
399 lines of code changed in 12 files:
-
DIST:
DI_compress_matrix.cxx (+10 -10),
DI_dna_shamos.cxx (+2 -2),
DI_matr.cxx (+146 -146),
DI_mldist.cxx (+24 -24),
DI_protdist.cxx (+32 -32),
DI_save_matr.cxx (+5 -5),
DI_view_matrix.cxx (+58 -58),
di_matr.hxx (+46 -46),
di_mldist.hxx (+24 -24),
di_protdist.hxx (+30 -30),
di_view_matrix.hxx (+15 -15),
distanalyse.cxx (+7 -7)
-
baderk
2008-06-09 15:38
#8
Rev.: 5391
-
54 lines of code changed in 4 files:
-
SEQ_QUALITY:
SQ_functions.cxx (+18 -1),
SQ_functions.h (+2),
SQ_main.cxx (+8)
-
lib/pictures:
seq_quality.fig (+26 -24)
-
westram
2008-06-06 14:23
#7
Rev.: 5390
-
33822 lines of code changed in 328 files:
-
README (+8 -41),
arb_README.txt (+82 -82),
arb_README_gcc.txt (+11 -11),
arb_install.sh (+303 -303)
-
AISC:
aisc.c (+302 -303),
aisc_commands.c (+25 -25),
aisc_var_ref.c (+213 -216)
-
AISC_COM:
keys.README (+45 -45),
pb_com.aisc (+109 -109)
-
AISC_COM/AISC:
aisc.pa (+98 -98),
aisc_com.pa (+125 -125),
aisc_debug_globals.pa (+51 -51),
aisc_global.pa (+110 -110),
aisc_server.pa (+836 -836),
keys.README (+46 -46)
-
AISC_COM/C:
aisc_server.h (+4 -5),
client.c (+85 -87),
client_privat.h (+23 -23),
debug.c (+76 -77),
server.c (+97 -97),
struct_man.c (+14 -14)
-
ALEIO:
embl-tabl.c (+236 -236),
fasta-tabl.c (+209 -209),
gb-tabl.c (+227 -227),
getopt.h (+73 -73),
getopt1.c (+80 -80),
hash.c (+71 -71),
hash.h (+2 -2),
ring.h (+18 -18),
tabl-embl.c (+139 -139),
tabl-fasta.c (+101 -101),
tabl-gb.c (+199 -199)
-
ARBDB:
Synchronized_Alignments.txt (+22 -22),
adReference.c (+16 -19),
adRevCompl.c (+19 -23),
admath.c (+14 -15),
adoptimize.c (+222 -221),
adseqcompr.c (+12 -12),
adsort.c (+28 -28),
adsystem.c (+6 -7),
adtune.c (+14 -15)
-
ARBDB/EXAMPLES:
all_spec_names.c (+24 -24),
read_all_sequences.c (+29 -28),
rnanames.c (+5 -5),
write_all_species.c (+9 -9)
-
ARBDBPP:
adtali.cxx (+102 -102),
adtools.hxx (+150 -153),
adtsequence.cxx (+58 -60),
liste.cxx (+51 -61)
-
ARBDB_COMPRESS:
AC_main.cxx (+95 -103),
AC_toys_n_tools.cxx (+108 -127),
AC_tree.cxx (+459 -465),
DEBUG_tools.cxx (+62 -62),
ac.hxx (+127 -134)
-
AWDEMO:
demo.cxx (+31 -31),
demo.hxx (+23 -24)
-
AWT:
AWT_asciiprint.cxx (+8 -8),
AWT_changekey.cxx (+5 -8),
AWT_codon_table.cxx (+151 -151),
AWT_irstree.cxx (+44 -41),
AWT_iupac.cxx (+2 -3),
AWT_tree_cmp.cxx (+20 -20),
AWT_www.cxx (+9 -9),
awt_asciiprint.hxx (+13 -13),
awt_automata.hxx (+18 -16),
awt_map_key.hxx (+7 -5),
awt_nei.hxx (+36 -36),
awt_seq_colors.hxx (+20 -16),
awt_tree_cmp.hxx (+19 -17),
awtfilter.hxx (+20 -19)
-
AWTC:
AWTC_ClustalV.cxx (+111 -116),
AWTC_seq_search.cxx (+19 -24),
awtc_ClustalV.hxx (+23 -4),
awtc_constructSequence.hxx (+17 -9),
awtc_fast_aligner.hxx (+14 -14),
awtc_next_neighbours.hxx (+15 -13)
-
AWTI:
awti_exp_local.hxx (+5 -5),
awti_export.hxx (+17 -16)
-
BUGEX:
bugex.h (+2 -2)
-
CAT:
CAT_tree.cxx (+191 -191),
cat_tree.hxx (+42 -42)
-
CONSENSUS_TREE:
CT_ctree.cxx (+41 -41),
CT_dtree.cxx (+30 -30),
CT_hash.cxx (+149 -150),
CT_hash.hxx (+3 -4),
CT_ntree.cxx (+143 -151),
CT_ntree.hxx (+9 -10),
CT_part.hxx (+18 -18),
CT_rbtree.cxx (+67 -67),
CT_rbtree.hxx (+3 -7),
help.cxx (+8 -8)
-
CONVERTALN:
alma.c (+640 -640),
date.c (+206 -206),
gcg.c (+170 -170),
genbank.c (+773 -773),
global.h (+12 -12),
macke.c (+562 -562),
main.c (+221 -221),
mg.c (+888 -888),
paup.c (+253 -254),
phylip.c (+186 -187),
printable.c (+210 -210),
routines.c (+38 -39),
swissprot.c (+619 -620),
truncate.c (+13 -13),
util.c (+242 -242),
vaxdate.c (+215 -216)
-
DBSERVER:
db_server.cxx (+7 -7)
-
DIST:
DI_dna_shamos.cxx (+3 -9),
DI_mldist.cxx (+232 -233),
DI_protdist.cxx (+722 -684),
DI_save_matr.cxx (+2 -2),
di_mldist.hxx (+56 -56),
di_protdist.hxx (+74 -70),
di_view_matrix.hxx (+44 -41),
distanalyse.cxx (+65 -68)
-
EDIT:
edit.hxx (+132 -128),
edit_naligner.cxx (+28 -29),
edit_tools.cxx (+426 -470)
-
EDIT4:
ED4_base.cxx (+87 -92),
ED4_block.cxx (+5 -7),
ED4_cursor.cxx (+81 -82),
ED4_list.cxx (+30 -35),
ED4_manager.cxx (+420 -504),
ED4_members.cxx (+48 -55),
ED4_mini_classes.cxx (+22 -29),
config_beschr.txt (+28 -28),
ed4_block.hxx (+29 -14),
ed4_objects.hxx (del)
-
EISPACK:
eispack.cxx (+6623 -6623),
f2c.h (+77 -77)
-
GDEHELP:
ARB_GDEmenus.source (+1 -1)
-
GDEHELP/DATA_FILES:
enzymes (+8 -8)
-
GDEHELP/MENUS:
pretty_print.menu (+1 -1),
warning.menu (+7 -7)
-
GENOM:
GEN_graphic.hxx (+2 -2)
-
GENOM_IMPORT:
GAARB.cpp (+367 -367),
GAARB.h (+40 -40),
GADDBJ.cpp (+935 -935),
GADDBJ.h (+48 -48),
GAEmbl.cpp (+830 -830),
GAEmbl.h (+22 -22),
GAFile.cpp (+196 -196),
GAFile.h (+91 -91),
GAGenBank.cpp (+734 -734),
GAGenBank.h (+21 -21),
GAGenomImport.cpp (+54 -55),
GALogger.cpp (+43 -43),
GALogger.h (+17 -17),
GASourceFileSwitcher.cpp (+55 -55),
GASourceFileSwitcher.h (+19 -19)
-
GL/glpng:
glpng.c (+483 -483),
glpng.h (+39 -39)
-
HELP_SOURCE/genhelp:
standard.header (+3 -3)
-
MERGE:
merge.hxx (+2 -2)
-
MULTI_PROBE:
MP_GenerationDuplicates.cxx (+4 -5),
MP_list.cxx (+23 -40),
MP_permute.cxx (+1 -1),
MP_probe_tabs.cxx (+4 -4),
mp_proto.hxx (+2 -3),
mpdefs.h (+40 -40)
-
NTREE:
ad_spec.hxx (+1 -1),
ap_conservProfile2Gnuplot.hxx (+10 -16),
ap_csp_2_gnuplot.hxx (+7 -11),
ntree.hxx (+4 -4)
-
PARSIMONY:
AP_buffer.cxx (+1 -2),
AP_buffer.hxx (+75 -75),
AP_main.cxx (+8 -9),
GA_genetic.hxx (+85 -88),
GA_main.cxx (+169 -173),
GA_window.cxx (+67 -68),
PARS_debug.cxx (+6 -6),
PARS_dtree.cxx (+13 -14),
ap_tree_nlen.hxx (+93 -90),
pars_debug.hxx (+2 -5),
pars_dtree.hxx (+11 -11),
pars_main.hxx (+5 -6),
ph_seq_pars.hxx (+12 -12)
-
PERL_SCRIPTS/ARBTOOLS/IFTHELP:
format_dssp.pl (+68 -68)
-
PERL_SCRIPTS/MAUS:
Maus.pm (+149 -150),
mausdriver.pl (+13 -13)
-
PERL_SCRIPTS/SPECIES:
markSpecies.pl (+4 -4)
-
PHYLO:
PH_data.cxx (+30 -34),
ph_seq_pars.hxx (+15 -14)
-
PRIMER_DESIGN:
PRD_Design.cxx (+75 -75),
PRD_Item.cxx (+30 -30),
PRD_Item.hxx (+13 -14),
PRD_Node.hxx (+8 -9),
PRD_Range.hxx (+13 -14),
PRD_SequenceIterator.cxx (+49 -49),
PRD_SequenceIterator.hxx (+9 -10),
primer_design.cxx (+48 -49)
-
PROBE:
PT_etc.cxx (+6 -6),
PT_family.cxx (+26 -26),
PT_match.cxx (+47 -49),
PT_new_design.cxx (+206 -190),
probe_debug.cxx (+16 -16)
-
PROBE_COM:
keys.README (+45 -45)
-
PROBE_DESIGN:
probe_design.hxx (+1 -1)
-
PROBE_SET:
ps_database.hxx (+129 -129),
ps_make_sample_db.cxx (+2 -2),
ps_node.cxx (+25 -25),
ps_node.hxx (+69 -69)
-
PROBE_WEB/CLIENT:
Toolkit.java (+13 -13)
-
READSEQ:
readseq.c (+8 -8)
-
RNA3D:
RNA3D_Global.hxx (+11 -12),
RNA3D_Graphics.hxx (+3 -4),
RNA3D_Interface.cxx (+94 -94),
RNA3D_OpenGLEngine.cxx (+95 -96),
RNA3D_OpenGLGraphics.hxx (+3 -4),
RNA3D_Renderer.cxx (+161 -161),
RNA3D_Textures.cxx (+7 -8)
-
SECEDIT:
SEC_gc.hxx (+2 -2)
-
SEER:
SEER_arb.cxx (+3 -3),
SEER_connect.cxx (+116 -118),
SEER_interface.cxx (+53 -53),
SEER_main.cxx (+157 -157),
SEER_to_seer.cxx (+271 -271),
seer.hxx (+32 -32),
seer_interface.hxx (+73 -74)
-
SERVERCNTRL:
servercntrl.c (+21 -18)
-
SH:
example_batch_probe_match.sh (+9 -10)
-
SL/DB_SCANNER:
db_scanner.cxx (+22 -24)
-
STAT:
ST_ml.cxx (+41 -41),
st_window.hxx (+16 -16)
-
TEST:
D_awt_graphic_designer.cxx (+21 -21),
D_classes.cxx (+61 -61),
d_awt_graphic_designer.hxx (+18 -18),
d_classes.hxx (+24 -23),
test.cxx (+44 -44),
test.hxx (+121 -121)
-
TESTAWT:
TB_extern.cxx (+165 -162),
tb_extern.hxx (+15 -13)
-
TESTVECTORFONT:
TB_extern.cxx (+161 -186),
tb_extern.hxx (+19 -17)
-
TOOLS:
arb_2_ascii.cxx (+1 -1),
arb_2_bin.cxx (+1 -1),
arb_a2ps.c (+317 -317),
arb_dnarates.c (+57 -60),
arb_newick_2_otb.cxx (+17 -17),
arb_perf_test.cxx (+17 -17),
arb_primer.cxx (+253 -253),
arb_replace.cxx (+20 -20),
arb_swap_rnastr.cxx (+95 -95)
-
TREE_COMPRESS:
tc.hxx (+121 -121)
-
TRS:
tree_lib.cxx (+539 -540),
tree_lib.hxx (+12 -13),
trs_server.cxx (+187 -187)
-
WETC:
WETC_main.cxx (+10 -10)
-
WINDOW:
AW_device.cxx (+121 -118),
AW_nawar.cxx (+47 -50),
AW_print.cxx (+22 -26),
AW_xfigfont.cxx (+473 -523),
AW_xfont.cxx (+21 -22),
GLwDrawA.h (+94 -95),
aw_at.hxx (+30 -30),
aw_awar.hxx (+26 -21),
aw_commn.hxx (+4 -4),
aw_keysym.hxx (+32 -34),
aw_root.hxx (+1 -1),
aw_window.hxx (+31 -39),
aw_xfigfont.hxx (+15 -11)
-
doc:
a2ps.README (+9 -9)
-
etc:
extendeds (+10 -10),
files (+21 -21)
-
lib:
GPL.txt (+7 -7),
arb_tcp_org.dat (+34 -34),
config.SunOS (+15 -15)
-
lib/export:
ae2.eft (+3 -3),
embl.eft (+1 -1),
fasta.eft (+2 -2),
fasta_NCBI_sequin.eft (+1 -1),
fasta_wide.eft (+2 -2),
gcg.eft (+1 -1),
genbank.eft (+1 -1),
genbank_list.eft (+1 -1),
paup.eft (+3 -3),
phylip.eft (+3 -3),
pir.eft (+2 -2),
xml.eft (+1 -1)
-
lib/import:
ae2.ift (+3 -3),
bergey.ift (+60 -60),
dewachter.ift (+57 -57),
dnasis.ift (+8 -8),
dssp_2nd_struct.ift (+3 -3),
dssp_2nd_struct2.ift2 (+35 -35),
dssp_all.ift (+3 -3),
dssp_all2.ift2 (+38 -38),
dssp_sequence.ift (+3 -3),
dssp_sequence2.ift2 (+35 -35),
ebi_multi.ift (+3 -3),
ebi_silva.ift (+111 -111),
fasta.ift (+16 -16),
fasta_wgap.ift (+15 -15),
gcg-rsf.ift (+65 -65),
gcg-rsf_pir.ift (+55 -55),
gcg-rsf_transl.ift (+68 -68),
gcg_seq_only.ift (+11 -11),
gde.ift (+12 -12),
gde_flat.ift (+11 -11),
genbank_multi.ift (+3 -3),
genbank_old.ift (+86 -86),
genbank_prot_from_translation_field.ift (+85 -85),
genbank_silva.ift (+100 -100),
genprot.ift (+18 -18),
licor_sequencer.ift (+7 -7),
licor_wl.ift (+27 -27),
licor_wl_new.ift (+27 -27),
nexus.ift (+3 -3),
nexus2.ift2 (+12 -12),
pir.ift (+51 -51),
rdp.ift (+197 -197),
rdp_old.ift (+111 -111),
universal_dna.ift (+5 -5),
universal_lower_case_dna.ift (+5 -5)
-
lib/import/nonformats:
longebi.ift (+322 -322),
longgenbank.ift (+306 -306)
-
lib/inputMasks:
main_fields.mask (+4 -4),
main_seq_info.mask (+6 -6)
-
lib/sellists:
README (+1 -1),
mod_fields.sellst (+9 -9),
mod_fields_common.sellst (+1 -1),
mod_fields_gc.sellst (+6 -6),
mod_gene_fields.sellst (+3 -3),
srt_aci.sellst (+4 -4)
-
lib/submit:
embl_newsubmission_wl (+5 -5)
-
util:
README (+12 -12),
arb_compress (+4 -4)
-
westram
2008-06-06 14:22
#6
Rev.: 5389
-
258 lines of code changed in 1 file:
-
SOURCE_TOOLS:
tabBrake.pl (new 258)
-
westram
2008-06-06 14:22
#5
Rev.: 5388
-
1 lines of code changed in 1 file:
-
SOURCE_TOOLS:
.cvsignore (+1 -1)
-
westram
2008-06-06 14:21
#4
Rev.: 5387
-
14 lines of code changed in 1 file:
-
westram
2008-06-06 14:20
#3
Rev.: 5386
-
0 lines of code changed in 8 files:
-
etc:
admin (del),
arb_changes (del),
buglist (del),
fopras (del),
history (del),
machine_compare (del),
perftest (del),
todo (del)
-
westram
2008-06-06 14:13
#2
Rev.: 5385
-
0 lines of code changed in 2 files:
-
HELP_SOURCE/oldhelp:
pfold.hlp (-5),
pfold_sai.hlp (-3)
-
westram
2008-06-06 10:59
#1
Rev.: 5384
-
0 lines of code changed in 1 file: